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maxscheurer / pycontact

Analysis of non-covalent interactions in MD trajectories
https://pycontact.github.io/
GNU General Public License v3.0
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tpr/xtc support #55

Closed wrmartin closed 6 years ago

wrmartin commented 6 years ago

This looks like a great tool. I noticed the example data supplied has a tpr/xtc set, but they will not load. Is there a plan for support in the future?

maxscheurer commented 6 years ago

tpr/xtc loading is definitely supported since we just use MDAnalysis to load the trajectory. Try to specify the following selections: selection1: segid seg_0_Protein_chain_U selection2: segid seg_1_Protein_chain_R

If you want to find out the segids in your system, open an IPython shell and execute:

import MDAnalysis as mda
u = mda.Universe("your_tpr_file.tpr")
print(u.segments)

Please let me know if you have further issues.

wrmartin commented 6 years ago

Ah! Ok, so it wasn't the file that was bad, it was the identification of segments. Thank you.